摘要：
Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

摘要：
Oilseed rape (Brassica napus L.) was formed similar to 7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent A(n) and C-n subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

摘要：
Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus.

摘要：
Plants must effectively defend against biotic and abiotic stresses to survive in nature. However, this defense is costly and is often accompanied by significant growth inhibition. How plants coordinate the fluctuating growth-defense dynamics is not well understood and remains a fundamental question. Jasmonate (JA) and gibberellic acid (GA) are important plant hormones that mediate defense and growth, respectively. Binding of bioactive JA or GA ligands to cognate receptors leads to proteasome-dependent degradation of specific transcriptional repressors (the JAZ or DELLA family of proteins), which, at the resting state, represses cognate transcription factors involved in defense (e.g., MYCs) or growth [e.g. phytochrome interacting factors (PIFs)]. In this study, we found that the coi1 JA receptor mutants of rice (a domesticated monocot crop) and Arabidopsis (a model dicot plant) both exhibit hallmark phenotypes of GA-hypersensitive mutants. JA delays GA-mediated DELLA protein degradation, and the della mutant is less sensitive to JA for growth inhibition. Overexpression of a selected group of JAZ repressors in Arabidopsis plants partially phenocopies GA-associated phenotypes of the coi1 mutant, and JAZ9 inhibits RGA (a DELLA protein) interaction with transcription factor PIF3. Importantly, the pif quadruple (pifq) mutant no longer responds to JA-induced growth inhibition, and overexpression of PIF3 could partially overcome JA-induced growth inhibition. Thus, a molecular cascade involving the COI1-JAZ-DELLA-PIF signaling module, by which angiosperm plants prioritize JA-mediated defense over growth, has been elucidated.

摘要：
The ideotype approach has been used in breeding programs at the International Rice Research Institute (IRRI) and in China to improve rice yield potential. First-generation new plant type (NPT) lines developed from tropical japonica at IRRI did not yield well because of limited biomass production and poor grain filling. Progress has been made in second-generation NPT lines developed by crossing elite indica with improved tropical japonica. Several second-generation NPT lines outyielded the first-generation NPT lines and indica check varieties. China's "super" rice breeding project has developed many F(1) hybrid varieties using a combination of the ideotype approach and intersubspecific heterosis. These hybrid varieties produced grain yield of 12 t ha(-1) in on-farm demonstration fields, 8-15% higher than the hybrid check varieties. The success of China's "super" hybrid rice was partially the result of assembling the good components of IRRI's NPT design in addition to the use of intersubspecific heterosis. For example, both designs focused on large panicle size, reduced tillering capacity, and improved lodging resistance. More importantly, improvement in plant type design was achieved in China's "super" hybrid rice by emphasizing the top three leaves and panicle position within a canopy in order to meet the demand of heavy panicles for a large source supply. The success of "super" hybrid rice breeding in China and progress in NPT breeding at IRRI suggest that the ideotype approach is effective for breaking the yield ceiling of an irrigated rice crop. (C) 2008 Elsevier B.V. All rights reserved.

摘要：
Agriculture faces great challenges to ensure global food security by increasing yields while reducing environmental costs(1,2). Here we address this challenge by conducting a total of 153 site-year field experiments covering the main agro-ecological areas for rice, wheat and maize production in China. A set of integrated soil-crop system management practices based on a modern understanding of crop ecophysiology and soil biogeochemistry increases average yields for rice, wheat and maize from 7.2 million grams per hectare (Mg ha(-1)), 7.2 Mg ha(-1) and 10.5 Mg ha(-1) to 8.5 Mg ha(-1), 8.9 Mg ha(-1) and 14.2 Mg ha(-1), respectively, without any increase in nitrogen fertilizer. Model simulation and life-cycle assessment(3) show that reactive nitrogen losses and greenhouse gas emissions are reduced substantially by integrated soil-crop system management. If farmers in China could achieve average grain yields equivalent to 80% of this treatment by 2030, over the same planting area as in 2012, total production of rice, wheat and maize in China would be more than enough to meet the demand for direct human consumption and a substantially increased demand for animal feed, while decreasing the environmental costs of intensive agriculture.

摘要：
Applying biochar to soils may cause a win-win situation resulting in C sequestration and soil fertility improvement. The effect may be more evident in highly weathered and infertile tropical soils, but will be dependent on biochar quality. An Ultisol, typical to southern China, was used to evaluate amendment with biochars produced by a range of temperatures and durations, to investigate its effects on soil properties and plant growth. Rice straw-derived biochars were charred at temperatures from 250 to 450 degrees C for between 2 and 8 h. The increase of temperature caused smaller less structured (as viewed by SEM) fragments to form with less 0, H and aliphatic C functional groups, but more aromatic C as indicated by infrared spectroscopy. The mean residence time of biochars under controlled conditions (25 degrees C, 40% field capacity) was estimated from 244 to 1700 years, generally increasing with charring temperature and duration. Amendment of 1% biochar increased pH by 0.1-0.46 (P < 0.01) and CEC by 3.9-17.3% (P < 0.05), but had no effect on aggregate stability. In pot trials maize biomass was increased by 64% (without NPK) to 146% (with NPK) after biochar amendment. The study emphasizes that amendment with biochar can improve soil fertility at least in the short term. Future studies focusing on the persistence of biochar fertility in the field must explicitly take into account additional factors to transfer this technology. (C) 2011 Elsevier B.V. All rights reserved.

摘要：
Dietary supplementation of glutamine prevents intestinal dysfunction and atrophy in weanling piglets, but the underlying mechanism(s) are largely unknown. This study was conducted to test the hypothesis that weaning or glutamine may modulate expression of genes that are crucial for intestinal metabolism and function. In Expt. 1, we obtained small intestine from 28-d-old pigs weaned at 21 d of age and from age-matched suckling piglets. In Expt. 2, piglets were weaned at 21 d of age and then had free access to diets supplemented with 1% L-glutamine (wt:wt) or isonitrogenous L-alanine (control). At d 28, we collected small intestine for biochemical and morphological measurements and microarray analysis of gene expression using the Operon Porcine Genome Oligo set. Early weaning resulted in increased (52-346%) expression of genes related to oxidative stress and immune activation but decreased (35-77%) expression of genes related to macronutrient metabolism and cell proliferation in the gut. Dietary glutamine supplementation increased intestinal expression (120-124%) of genes that are necessary for cell growth and removal of oxidants, while reducing (34-75%) expression of genes that promote oxidative stress and immune activation. Functionally, the glutamine treatment enhanced intestinal oxidative-defense capacity (indicated by a 29% increase in glutathione concentration), prevented jejunal atrophy, and promoted small intestine growth (+12%) and body weight gain (+19%) in weaned piglets. These findings reveal coordinate alterations of gene expression in response to weaning and aid in providing molecular mechanisms for the beneficial effect of dietary glutamine supplementation to improve nutrition status in young mammals.

摘要：
With the recent availability of complete genomic sequences of many organisms, high-throughput and cost-efficient systems for gene cloning and functional analysis are in great demand. Although site-specific recombination-based cloning systems, such as Gateway cloning technology, are extremely useful for efficient transfer of DNA fragments into multiple destination vectors, the two-step cloning process is time consuming and expensive. Here, we report a zero background TA cloning system that provides simple and high-efficiency direct cloning of PCR-amplified DNA fragments with almost no self-ligation. The improved T-vector system takes advantage of the restriction enzyme XcmI to generate a T-overhang after digestion and the negative selection marker gene ccdB to eliminate the self-ligation background after transformation. We demonstrate the feasibility and flexibility of the technology by developing a set of transient and stable transformation vectors for constitutive gene expression, gene silencing, protein tagging, protein subcellular localization detection, and promoter fragment activity analysis in plants. Because the system can be easily adapted for developing specialized expression vectors for other organisms, zero background TA provides a general, cost-efficient, and high-throughput platform that complements the Gateway cloning system for gene cloning and functional genomics.

摘要：
Rice production in China has more than tripled in the past five decades mainly due in increased grain yield rather than increased planting area. This increase has come from the development of high-yielding varieties and improved crop management practices such as nitrogen fertilization and irrigation. However, yield stagnation of rice has been observed in the past ten years in China. As its population rises, China will need to produce about 20% more rice by 2030 in order to meet is domestic needs if rice consumption per capita stays at the current level. This is not an easy task because several trends and problems in the Chinese rice production system constrain the sustainable increase in total rice production. Key trends include a decline in arable land, increasing water scarcity, global climate change, labor shortages, and increasing comsumer demand for high-quality rice (which often comes from low-yielding varieties). The major problems confronting rice production in China are narrow genetic background, overuse of fertilizers and pesticides, breakdown of irrigation infrastructure, oversimplified crop management, and a weak extension system. Despite these challenges, good research strategies call drive increased rice production in China. These include the development of the new rice varieties with high yield potential, improvement of resistances to major diseases and insects, and to major abiotic stresses such as drought and heat, and the establishment of integrated crop management. We believe that a sustainable increase in rice production is achievable in China with the development of new technology through rice research.

摘要：
Increasing soil pollution problems have caused world-wide concerns. Large numbers of contaminants such as polycyclic aromatic hydrocarbons (PAHs), petroleum and related products, pesticides, chlorophenols and heavy metals enter the soil, posing a huge threat to human health and natural ecosystem. Chemical and physical technologies for soil remediation are either incompetent or too costly. Composting or compost addition can simultaneously increase soil organic matter content and soil fertility besides bioremediation, and thus is believed to be one of the most cost-effective methods for soil remediation. This paper reviews the application of composting/compost for soil bioremediation, and further provides a critical view on the effects of this technology on microbial aspects in contaminated soils. This review also discusses the future research needs for contaminated soils.

摘要：
Precise coordination between stamen and pistil development is essential to make a fertile flower. Mutations impairing stamen filament elongation, pollen maturation, or anther dehiscence will cause male sterility. Deficiency in plant hormone gibberellin (GA) causes male sterility due to accumulation of DELLA proteins, and GA triggers DELLA degradation to promote stamen development. Deficiency in plant hormone jasmonate (JA) also causes male sterility. However, little is known about the relationship between GA and JA in controlling stamen development. Here, we show that MYB21, MYB24, and MYB57 are GA-dependent stamen-enriched genes. Loss-of-function of two DELLAs RGA and RGL2 restores the expression of these three MYB genes together with restoration of stamen filament growth in GA-deficient plants. Genetic analysis showed that the myb21-t1 myb24-t1 myb57-t1 triple mutant confers a short stamen phenotype leading to male sterility. Further genetic and molecular studies demonstrate that GA suppresses DELLAs to mobilize the expression of the key JA biosynthesis gene DAD1, and this is consistent with the observation that the JA content in the young flower buds of the GA-deficient quadruple mutant ga1-3 gai-t6 rga-t2 rgl1-1 is much lower than that in the WT. We conclude that GA promotes JA biosynthesis to control the expression of MYB21, MYB24, and MYB57. Therefore, we have established a hierarchical relationship between GA and JA in that modulation of JA pathway by GA is one of the prerequisites for GA to regulate the normal stamen development in Arabidopsis.

摘要：
Excessive nitrogen (N) application to rice (Oryza sativa L.) crop in China causes environmental pollution, increases the cost of rice farming, reduces grain yield and contributes to global warming. Scientists from the International Rice Research Institute have collaborated with partners in China to improve rice N fertilization through site-specific N management (SSNM) in China since 1997. Field experiments and demonstration trials were conducted initially in Zhejiang province and gradually expanded to Guangdong, Hunan, Jiangsu, Hubei and Heilongjiang provinces. On average, SSNM reduced N fertilizer by 32% and increased grain yield by 5% compared with farmers' N practices. The yield increase was associated with the reduction in insect and disease damage and improved lodging resistance of rice crop under the optimal N inputs. The main reason for poor fertilizer N use efficiency of rice crop in China is that most rice farmers apply too much N fertilizer, especially at the early vegetative stage. We observed about 50% higher indigenous N supply capacity in irrigated rice fields in China than in other major rice-growing countries. Furthermore, yield response of rice crop to N fertilizer application is low in China, around 1.5 t ha(-1) on average. However, these factors were not considered by rice researchers and extension technicians in determining the N fertilizer rate for recommendation to rice farmers in China. After a decade of research on SSNM in China and other Asian rice-growing countries, we believe SSNM is a matured technology for improving both fertilizer N use efficiency and grain yield of rice crop. Our challenges are to further simplify the procedure of SSNM and to convince policy-makers of the effectiveness of this technology in order to facilitate a wider adoption of SSNM among rice farmers in China.

摘要：
Efficiency of nutrient utilization is high in neonates with normal birth weights but is reduced in those with intrauterine growth restriction (IUGR). However, the underlying mechanisms are largely unknown. This study was conducted with the piglet model and proteomics technology to test the hypothesis that IUGR affects expression of key proteins that regulate growth and development of the small intestine, liver, and muscle, the major organs involved in the digestion, absorption, and metabolism of dietary nutrients. Jejunum, liver, and gastrocnemius muscle were obtained from IUGR and normal birth-weight piglets at birth for analysis of proteomes using the 2-dimensional-PAGE MS technology. The results indicate that IUGR decreased the levels of proteins that regulate immune function (immunoglobulins and annexin A1), oxidative defense (peroxiredoxin 1, transferrin, and zeta-crystallin), intermediary metabolism (creatine kinase, alcohol dehydrogenase, L-lactate dehydrogenase, prostaglandin F synthase, apolipoprotein AI, catecho O-methyltransferase, and phosphoglycerate kinase 1), protein synthesis (eukaryotic translation initiation factor-3), and tissue growth (beta-actin, desmin, and keratin 10) in a tissue-specific manner. In addition, IUGR increased the levels of proteins that are involved in proteolysis (proteasome alpha-5 and alpha-1 subunits), response to oxidative stress (scavenger-receptor protein and alpha-1 acid glycoprotein), and ATP hydrolysis (F1-ATPase). These novel findings suggest that cellular signaling defects, redox imbalance, reduced protein synthesis, and enhanced proteolysis may be the major mechanisms responsible for abnormal absorption and metabolism of nutrients, as well as reduced growth and impaired development of the small intestine, liver, and muscle in IUGR neonates.